| leafs_1ptf_fastRelax_25 |
| ID: | 1507536403 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 495 (307.3) | ||
| Seq/Len: | 5.690 | ||
| Nf(neff/√len): | 32.9 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 5.690).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 30_E | 68_R | 4.184 | 1.00 |
| 63_V | 77_I | 2.444 | 1.00 |
| 9_K | 85_F | 2.239 | 1.00 |
| 7_L | 60_L | 1.962 | 1.00 |
| 33_F | 77_I | 1.950 | 1.00 |
| 1_E | 70_D | 1.722 | 1.00 |
| 34_W | 41_I | 1.705 | 1.00 |
| 3_Y | 64_F | 1.604 | 0.99 |
| 2_V | 28_L | 1.578 | 0.99 |
| 51_H | 70_D | 1.544 | 0.99 |
| 11_S | 28_L | 1.533 | 0.99 |
| 1_E | 66_R | 1.486 | 0.99 |
| 51_H | 54_H | 1.420 | 0.98 |
| 28_L | 70_D | 1.414 | 0.98 |
| 59_L | 80_E | 1.413 | 0.98 |
| 50_I | 77_I | 1.372 | 0.98 |
| 39_G | 44_M | 1.304 | 0.97 |
| 17_Q | 84_K | 1.281 | 0.96 |
| 81_F | 86_I | 1.272 | 0.96 |
| 21_A | 80_E | 1.255 | 0.95 |
| 25_V | 76_E | 1.255 | 0.95 |
| 9_K | 18_V | 1.213 | 0.94 |
| 6_F | 63_V | 1.209 | 0.94 |
| 30_E | 85_F | 1.180 | 0.93 |
| 5_L | 71_T | 1.173 | 0.93 |
| 34_W | 66_R | 1.158 | 0.92 |
| 50_I | 63_V | 1.147 | 0.92 |
| 12_T | 82_L | 1.146 | 0.92 |
| 18_V | 86_I | 1.142 | 0.91 |
| 71_T | 77_I | 1.133 | 0.91 |
| 68_R | 85_F | 1.130 | 0.91 |
| 17_Q | 80_E | 1.113 | 0.90 |
| 70_D | 78_H | 1.109 | 0.90 |
| 70_D | 76_E | 1.107 | 0.90 |
| 30_E | 66_R | 1.099 | 0.89 |
| 6_F | 50_I | 1.089 | 0.89 |
| 36_D | 83_R | 1.074 | 0.88 |
| 21_A | 34_W | 1.072 | 0.88 |
| 40_K | 52_L | 1.056 | 0.87 |
| 6_F | 78_H | 1.003 | 0.82 |
| 34_W | 62_V | 1.003 | 0.82 |
| 5_L | 17_Q | 1.002 | 0.82 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- See coupling matrix (for protein design or mutagenesis)
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3le1A | 2 | 0.9885 | 95.8 | 0.835 | Contact Map |
| 1ka5A | 1 | 1 | 95.7 | 0.835 | Contact Map |
| 1y51A | 3 | 0.977 | 95.6 | 0.837 | Contact Map |
| 3ihsA | 2 | 0.9425 | 95.5 | 0.838 | Contact Map |
| 1kklH | 3 | 0.9885 | 95.5 | 0.838 | Contact Map |
| 1pchA | 1 | 0.977 | 95.5 | 0.838 | Contact Map |
| 1sphA | 2 | 0.977 | 95.5 | 0.838 | Contact Map |
| 1ptfA | 1 | 1 | 95.3 | 0.84 | Contact Map |
| 3ccdA | 2 | 0.977 | 95.2 | 0.841 | Contact Map |
| 1u02A | 1 | 0.6207 | 13.1 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)